rs2819096

Positions:

• chr10-79947857-A-C
• chr10-79947857-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003019.5(SFTPD):​c.-3-1195T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,084 control chromosomes in the GnomAD database, including 30,443 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (30443 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

SFTPD (HGNC:10803): (surfactant protein D) The protein encoded by this gene is part of the innate immune response, protecting the lungs against inhaled microorganisms and chemicals. The encoded protein may also be involved in surfactant metabolism. [provided by RefSeq, Jul 2015]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.-3-1195T>G		intron_variant		ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.-3-1195T>G		intron_variant			XP_011538389.1
SFTPD	XM_011540088.3	c.-3-1195T>G		intron_variant			XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.-3-1195T>G		intron_variant		1	NM_003019.5	ENSP00000361366	P1
SFTPD	ENST00000444384.3	c.37-1195T>G		intron_variant		3		ENSP00000394325
	ENST00000421889.1	n.334-2171A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95312 AN: 151966 Hom.: 30396 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.612

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.627 AC: 95422 AN: 152084 Hom.: 30443 Cov.: 32 AF XY: 0.627 AC XY: 46647 AN XY: 74338

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.617

Alfa AF: 0.582 Hom.: 33702

Bravo AF: 0.632

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2819096; hg19: chr10-81707613;